We have demonstrated that chemoprotective diets containing turmeric (curcumin) and citrus (limonin) bioactives reduce chronic inflammation and colon cancer risk. With respect to cancer biology, recent observations demonstrate that crypt stem cells are the cells-of-origin of intestinal cancer. Since non-coding microRNA-mediated translational repression and changes to chromatin structure may be linked to the development of colon cancer, it is vital that the effect of chemopreventive diets on microRNAs, their messenger RNA (mRNA) targets, and epigenetic modifications on both the histone and DNA levels in intestinal stem cells be determined. However, to date, the effect of dietary botanicals on genome-wide chromatin epigenetic modifications, microRNAs, and mRNA populations in intestinal stem cells, crypts and tumors has not been determined. Therefore, we hypothesize that a chemoprotective diet, containing curcumin and/or the citrus bioactive limonin, will modulate the stem cell transcriptome, resulting in a favorable shift in disease progression. Aim 1 will use highly novel stem cell specific Lgr5-LacZ and Lgr-EGFP mice to quantify the number and spatio-temporal location of stem cells, DNA damage and targeted apoptosis in the colonic crypt at the initiation and tumor stages of colon carcinogenesis following exposure to diets containing curcumin, limonin, and their mixture. Aim 2 will use the Lgr5-EGFP mouse to investigate the effect of disease progression on microRNAs and their post-transcriptionally regulated mRNA targets in colonic stem cells, intact colonic crypts and tumors following carcinogen/inflammation or saline (control) exposure. Aim 3 will generate high-resolution genome- wide chromatin-state maps for (i) intestinal epithelial cell crypts, and (ii) colonic tumors using chromatin immunoprecipitation in order to assess the effect of diet and colitis-associated colon carcinogenesis on epigenetic modifications at both the histone and DNA levels. It is anticipated that novel stem cell signaling networks and markers will emerge from these studies. The proposed studies will promote our understanding of how botanicals impact critical signaling pathways during normal intestinal development and malignant transformation, including self-renewal of stem cells.